It seems to be a bit hit and miss for some reason. My 2011 E91 never had any problem with FAT32 or NTFS while others over on the UK E9x section just didn't have any luck with NTFS. The F31 loan car I have at the moment also has no problem with NTFS.

I do wonder if it's something to do with the machine you do the formatting on but that doesn't really make any logical sense...